From 2e8a3d2457978affb32cd72f838cc4d01a9d3242 Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Mon, 16 Feb 2026 16:15:56 +0000 Subject: [PATCH] Drop use of pkg_resources Removed in setuptools 82.0.0: https://setuptools.pypa.io/en/stable/history.html#v82-0-0 --- .../annotation_profiler/scripts/build_profile_indexes.py | 6 ------ tool_collections/taxonomy/find_diag_hits/find_diag_hits.py | 3 --- tools/lastz_paired_reads/lastz_paired_reads_wrapper.py | 3 --- tools/quality_filter/quality_filter.py | 4 ---- 4 files changed, 16 deletions(-) diff --git a/deprecated/tools/annotation_profiler/scripts/build_profile_indexes.py b/deprecated/tools/annotation_profiler/scripts/build_profile_indexes.py index a4fe4c602..d013b5d14 100644 --- a/deprecated/tools/annotation_profiler/scripts/build_profile_indexes.py +++ b/deprecated/tools/annotation_profiler/scripts/build_profile_indexes.py @@ -13,12 +13,6 @@ except ImportError: from md5 import new as md5 -#import BitSet from bx-python, try using eggs and package resources, fall back to any local installation -try: - from galaxy import eggs - import pkg_resources - pkg_resources.require( "bx-python" ) -except: pass #Maybe there is a local installation available from bx.bitset import BitSet #Define constants diff --git a/tool_collections/taxonomy/find_diag_hits/find_diag_hits.py b/tool_collections/taxonomy/find_diag_hits/find_diag_hits.py index 0b6b7e22b..9ede23cac 100644 --- a/tool_collections/taxonomy/find_diag_hits/find_diag_hits.py +++ b/tool_collections/taxonomy/find_diag_hits/find_diag_hits.py @@ -42,9 +42,6 @@ """ -from galaxy import eggs -import pkg_resources -pkg_resources.require( 'pysqlite' ) from pysqlite2 import dbapi2 as sqlite import string, sys, tempfile diff --git a/tools/lastz_paired_reads/lastz_paired_reads_wrapper.py b/tools/lastz_paired_reads/lastz_paired_reads_wrapper.py index c81967702..e7c3a2952 100644 --- a/tools/lastz_paired_reads/lastz_paired_reads_wrapper.py +++ b/tools/lastz_paired_reads/lastz_paired_reads_wrapper.py @@ -41,9 +41,6 @@ import optparse, os, subprocess, shutil, sys, tempfile, time from string import maketrans -from galaxy import eggs -import pkg_resources -pkg_resources.require( 'bx-python' ) from bx.seq.twobit import * from bx.seq.fasta import FastaReader from galaxy.util.bunch import Bunch diff --git a/tools/quality_filter/quality_filter.py b/tools/quality_filter/quality_filter.py index af2b70c4d..29a1e5586 100644 --- a/tools/quality_filter/quality_filter.py +++ b/tools/quality_filter/quality_filter.py @@ -8,10 +8,6 @@ from __future__ import division -from galaxy import eggs -import pkg_resources -pkg_resources.require( "lrucache" ) -import numpy import sys import os, os.path